.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data87.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 388 patterns found. (out of a total of 500 sites) . 107 sites without polymorphism (21.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20824.1169] [GTR parameters ] . ( 1 sec) [ -20449.3050] [Alpha ][ 0.500960] . ( 1 sec) [ -19947.8037] [ 3622] [depth= 8] . ( 1 sec) [ -19534.9794] [ 3614] [depth= 7] . ( 1 sec) [ -17029.5973] [ 3590] [depth= 4] . ( 1 sec) [ -16342.5755] [ 3586] [depth= 5] . ( 1 sec) [ -16080.8236] [ 3548] [depth= 5] . ( 1 sec) [ -16046.1500] [ 3544] [depth= 5] . ( 1 sec) [ -16023.7188] [ 3527] [depth= 4] . ( 1 sec) [ -15929.1196] [ 3514] [depth= 1] . ( 1 sec) [ -15800.8040] [ 3459] [depth= 1] . ( 1 sec) [ -15610.6352] [ 3418] [depth= 3] . ( 1 sec) [ -14940.4972] [ 3280] [depth= 13] . ( 1 sec) [ -14861.8003] [ 3281] [depth= 12] . ( 1 sec) [ -14607.2644] [ 3239] [depth= 5] . ( 1 sec) [ -14549.7801] [ 3234] [depth= 2] . ( 1 sec) [ -14488.6146] [ 3232] [depth= 1] . ( 1 sec) [ -14382.3870] [ 3189] [depth= 8] . ( 2 sec) [ -14374.9878] [ 3185] [depth= 2] . ( 2 sec) [ -14286.6897] [ 3180] [depth= 4] . ( 2 sec) [ -14258.6987] [ 3177] [depth= 2] . ( 2 sec) [ -14256.9670] [ 3171] [depth= 9] . ( 2 sec) [ -14113.2040] [ 3117] [depth= 6] . ( 2 sec) [ -14102.1284] [ 3114] [depth= 1] . ( 2 sec) [ -14074.3717] [ 3089] [depth= 10] . ( 2 sec) [ -13571.2291] [ 2945] [depth= 10] . ( 2 sec) [ -13543.0161] [ 2952] [depth= 6] . ( 2 sec) [ -13534.6525] [ 2910] [depth= 10] . ( 2 sec) [ -13300.6871] [ 2882] [depth= 2] . ( 2 sec) [ -13160.2879] [ 2852] [depth= 3] . ( 2 sec) [ -13066.2955] [ 2816] [depth= 2] . ( 2 sec) [ -12937.0002] [ 2760] [depth= 11] . ( 2 sec) [ -12830.6875] [ 2768] [depth= 1] . ( 2 sec) [ -12646.1045] [ 2712] [depth= 2] . ( 2 sec) [ -12621.7270] [ 2696] [depth= 1] . ( 2 sec) [ -11990.7458] [ 2548] [depth= 5] . ( 2 sec) [ -11963.6379] [ 2546] [depth= 10] . ( 2 sec) [ -11748.3673] [ 2500] [depth= 9] . ( 2 sec) [ -11626.6053] [ 2460] [depth= 3] . ( 2 sec) [ -11623.6932] [ 2459] [depth= 1] . ( 2 sec) [ -11601.2517] [ 2447] [depth= 4] . ( 2 sec) [ -11568.4421] [ 2448] [depth= 1] . ( 2 sec) [ -11469.9810] [ 2415] [depth= 1] . ( 3 sec) [ -11464.9680] [ 2420] [depth= 1] . ( 3 sec) [ -11267.0178] [ 2335] [depth= 5] . ( 3 sec) [ -11258.6417] [ 2334] [depth= 1] . ( 3 sec) [ -11255.1158] [ 2334] [depth= 1] . ( 3 sec) [ -11149.3732] [ 2309] [depth= 2] . ( 3 sec) [ -11149.2042] [ 2310] [depth= 1] . ( 3 sec) [ -11140.1953] [ 2302] [depth= 5] . ( 3 sec) [ -11000.9245] [ 2271] [depth= 1] . ( 3 sec) [ -10819.6100] [ 2240] [depth= 6] . ( 3 sec) [ -10599.1326] [ 2238] [depth= 3] . ( 3 sec) [ -10302.9439] [ 2146] [depth= 11] . ( 3 sec) [ -10302.8628] [ 2148] [depth= 1] . ( 3 sec) [ -10173.3361] [ 2092] [depth= 7] . ( 3 sec) [ -9769.1585] [ 2095] [depth= 2] . ( 3 sec) [ -9585.4025] [ 2059] [depth= 3] . ( 3 sec) [ -9509.6834] [ 2021] [depth= 3] . ( 3 sec) [ -9477.9992] [ 2004] [depth= 1] . ( 3 sec) [ -9451.5470] [ 1992] [depth= 1] . ( 3 sec) [ -9431.7968] [ 1970] [depth= 1] . ( 3 sec) [ -9389.3339] [ 1925] [depth= 5] . ( 4 sec) [ -9372.7706] [ 1920] [depth= 1] . ( 4 sec) [ -9370.1962] [ 1918] [depth= 1] . ( 4 sec) [ -8977.4242] [ 1871] [depth= 1] . ( 4 sec) [ -8658.1683] [ 1852] [depth= 2] . ( 4 sec) [ -8573.9885] [ 1813] [depth= 6] . ( 4 sec) [ -8570.5676] [ 1816] [depth= 1] . ( 4 sec) [ -8387.4610] [ 1756] [depth= 3] . ( 4 sec) [ -8355.2529] [ 1744] [depth= 1] . ( 4 sec) [ -8354.2636] [ 1742] [depth= 1] . ( 4 sec) [ -8293.0073] [ 1737] [depth= 2] . ( 4 sec) [ -8276.0515] [ 1726] [depth= 3] . ( 4 sec) [ -8246.0245] [ 1727] [depth= 1] . ( 4 sec) [ -8239.9416] [ 1731] [depth= 2] . ( 4 sec) [ -8184.2623] [ 1694] [depth= 4] . ( 4 sec) [ -8180.8380] [ 1699] [depth= 1] . ( 5 sec) [ -8112.7281] [Branch lengths ] . ( 5 sec) [ -8108.2866] [GTR parameters ] . ( 5 sec) [ -8090.7753] [Alpha ][ 0.786637] . ( 5 sec) [ -8081.5880] [ 1701] [depth= 2] . ( 5 sec) [ -8024.9431] [ 1675] [depth= 1] . ( 5 sec) [ -8024.5848] [ 1669] [depth= 1] . ( 5 sec) [ -8012.9454] [ 1657] [depth= 1] . ( 5 sec) [ -8012.7252] [ 1657] [depth= 1] . ( 6 sec) [ -8011.7966] [ 1656] [depth= 1] . ( 6 sec) [ -7992.0603] [ 1639] [depth= 2] . ( 6 sec) [ -7933.0877] [ 1613] [depth= 1] . ( 6 sec) [ -7931.8873] [ 1611] [depth= 1] . ( 6 sec) [ -7931.5420] [ 1613] [depth= 1] . ( 6 sec) [ -7930.8651] [ 1612] [depth= 1] . ( 6 sec) [ -7930.2766] [ 1613] [depth= 1] . ( 7 sec) [ -7927.8402] [ 1617] [depth= 1] . ( 7 sec) [ -7927.7317] [ 1616] [depth= 1] . ( 7 sec) [ -7927.4073] [ 1617] [depth= 1] . ( 7 sec) [ -7926.2831] [ 1619] [depth= 1] . ( 7 sec) [ -7924.8777] [ 1622] [depth= 1] . ( 8 sec) [ -7923.8207] [ 1621] [depth= 1] . ( 8 sec) [ -7923.6322] [ 1618] [depth= 1] . ( 8 sec) [ -7914.6170] [Branch lengths ] . ( 8 sec) [ -7914.4415] [GTR parameters ] . ( 9 sec) [ -7913.9068] [Alpha ][ 0.853725] . ( 10 sec) [ -7913.7742] [ 1621] [depth= 1] . ( 10 sec) [ -7913.7392] [ 1621] [depth= 1] . ( 11 sec) [ -7911.6831] [Branch lengths ] . ( 12 sec) [ -7911.6816] [GTR parameters ] . ( 12 sec) [ -7911.6704] [Alpha ][ 0.864130] . ( 15 sec) [ -7904.6406] [Branch lengths ] . ( 20 sec) [ -7904.5889] [ 1619] [depth= 1] . ( 32 sec) [ -7896.6165] [Branch lengths ] . ( 33 sec) [ -7896.6109] [GTR parameters ] . ( 33 sec) [ -7896.6078] [Alpha ][ 0.869622] . ( 50 sec) [ -7896.4634] [Branch lengths ] . ( 50 sec) [ -7896.4634] [Topology ] . ( 51 sec) [ -7896.4243] [Topology ] . ( 51 sec) [ -7896.4027] [Topology ] . ( 52 sec) [ -7896.3993] [Topology ] . ( 53 sec) [ -7896.3984] [Topology ] . ( 53 sec) [ -7896.3982] [GTR parameters ] . ( 53 sec) [ -7896.3979] [Alpha ][ 0.871179] . ( 53 sec) [ -7896.3979] [Topology ] . ( 54 sec) [ -7896.3976] [Topology ] . ( 54 sec) [ -7896.3976] [GTR parameters ] . ( 54 sec) [ -7896.3976] [Alpha ][ 0.871179] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -7896.3975] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7896.397485. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19274.8414] [GTR parameters ] . ( 1 sec) [ -18933.9361] [Alpha ][ 0.500960] . ( 1 sec) [ -18637.7638] [ 3690] [depth= 3] . ( 1 sec) [ -18465.8124] [ 3671] [depth= 3] . ( 1 sec) [ -16420.2146] [ 3659] [depth= 4] . ( 1 sec) [ -16328.1866] [ 3641] [depth= 6] . ( 1 sec) [ -16170.0688] [ 3591] [depth= 2] . ( 1 sec) [ -16063.2655] [ 3566] [depth= 4] . ( 1 sec) [ -15915.6575] [ 3555] [depth= 4] . ( 1 sec) [ -15732.8923] [ 3521] [depth= 2] . ( 1 sec) [ -15668.7501] [ 3515] [depth= 1] . ( 1 sec) [ -15525.6535] [ 3467] [depth= 7] . ( 1 sec) [ -15460.0746] [ 3465] [depth= 3] . ( 1 sec) [ -15315.0035] [ 3410] [depth= 1] . ( 1 sec) [ -15218.5159] [ 3404] [depth= 2] . ( 1 sec) [ -14935.0055] [ 3311] [depth= 10] . ( 1 sec) [ -14770.1255] [ 3266] [depth= 8] . ( 1 sec) [ -14286.1873] [ 3212] [depth= 2] . ( 1 sec) [ -13969.5190] [ 3157] [depth= 2] . ( 1 sec) [ -13911.4685] [ 3163] [depth= 1] . ( 1 sec) [ -13883.5219] [ 3091] [depth= 1] . ( 2 sec) [ -13609.2731] [ 3031] [depth= 7] . ( 2 sec) [ -13062.4352] [ 2978] [depth= 15] . ( 2 sec) [ -12945.1388] [ 2929] [depth= 4] . ( 2 sec) [ -12641.0165] [ 2829] [depth= 11] . ( 2 sec) [ -12619.2855] [ 2834] [depth= 1] . ( 2 sec) [ -12433.2029] [ 2786] [depth= 11] . ( 2 sec) [ -12380.8058] [ 2781] [depth= 1] . ( 2 sec) [ -12280.9380] [ 2761] [depth= 7] . ( 2 sec) [ -12006.4143] [ 2636] [depth= 11] . ( 2 sec) [ -12006.1274] [ 2645] [depth= 1] . ( 2 sec) [ -11937.0732] [ 2625] [depth= 4] . ( 2 sec) [ -11864.0553] [ 2630] [depth= 2] . ( 2 sec) [ -11546.5278] [ 2617] [depth= 2] . ( 2 sec) [ -11403.1694] [ 2618] [depth= 1] . ( 2 sec) [ -11307.6239] [ 2555] [depth= 6] . ( 2 sec) [ -11039.0893] [ 2518] [depth= 4] . ( 2 sec) [ -10956.3916] [ 2450] [depth= 8] . ( 2 sec) [ -10816.0157] [ 2458] [depth= 1] . ( 2 sec) [ -10789.4759] [ 2446] [depth= 1] . ( 2 sec) [ -10403.3522] [ 2390] [depth= 2] . ( 2 sec) [ -10351.0120] [ 2333] [depth= 13] . ( 2 sec) [ -10268.8242] [ 2307] [depth= 1] . ( 3 sec) [ -10102.4374] [ 2308] [depth= 9] . ( 3 sec) [ -10084.4489] [ 2300] [depth= 1] . ( 3 sec) [ -9827.8067] [ 2218] [depth= 6] . ( 3 sec) [ -9764.1657] [ 2219] [depth= 1] . ( 3 sec) [ -9761.8072] [ 2215] [depth= 1] . ( 3 sec) [ -9735.7958] [ 2209] [depth= 2] . ( 3 sec) [ -9536.7598] [ 2154] [depth= 9] . ( 3 sec) [ -9519.9987] [ 2125] [depth= 1] . ( 3 sec) [ -9473.0361] [ 2123] [depth= 2] . ( 3 sec) [ -9471.6097] [ 2117] [depth= 3] . ( 3 sec) [ -9334.9851] [ 2079] [depth= 7] . ( 3 sec) [ -9208.6159] [ 2046] [depth= 1] . ( 3 sec) [ -9207.2928] [ 2023] [depth= 5] . ( 3 sec) [ -9083.8328] [ 1970] [depth= 3] . ( 3 sec) [ -8994.1414] [ 1980] [depth= 1] . ( 3 sec) [ -8785.2734] [ 1900] [depth= 3] . ( 3 sec) [ -8743.2403] [ 1877] [depth= 3] . ( 3 sec) [ -8727.2610] [ 1875] [depth= 1] . ( 3 sec) [ -8675.8731] [ 1853] [depth= 6] . ( 3 sec) [ -8523.6762] [ 1817] [depth= 6] . ( 3 sec) [ -8516.5383] [ 1815] [depth= 1] . ( 3 sec) [ -8508.9972] [ 1812] [depth= 1] . ( 4 sec) [ -8505.1591] [ 1815] [depth= 1] . ( 4 sec) [ -8494.1399] [ 1803] [depth= 1] . ( 4 sec) [ -8490.8607] [ 1810] [depth= 1] . ( 4 sec) [ -8429.2828] [ 1795] [depth= 3] . ( 4 sec) [ -8428.0177] [ 1796] [depth= 2] . ( 4 sec) [ -8410.1751] [ 1783] [depth= 2] . ( 4 sec) [ -8406.3536] [ 1784] [depth= 1] . ( 4 sec) [ -8385.6381] [ 1774] [depth= 1] . ( 4 sec) [ -8255.0852] [ 1747] [depth= 3] . ( 4 sec) [ -8235.6751] [ 1736] [depth= 1] . ( 4 sec) [ -8235.0075] [ 1737] [depth= 1] . ( 4 sec) [ -8175.6658] [ 1699] [depth= 5] . ( 4 sec) [ -8150.7273] [ 1688] [depth= 2] . ( 4 sec) [ -8148.7327] [ 1690] [depth= 1] . ( 4 sec) [ -8013.3616] [Branch lengths ] . ( 5 sec) [ -8011.6282] [GTR parameters ] . ( 5 sec) [ -7992.7507] [Alpha ][ 0.794691] . ( 5 sec) [ -7989.3810] [ 1677] [depth= 1] . ( 5 sec) [ -7974.8206] [ 1660] [depth= 1] . ( 5 sec) [ -7974.7285] [ 1660] [depth= 1] . ( 5 sec) [ -7974.6921] [ 1661] [depth= 2] . ( 5 sec) [ -7974.5555] [ 1666] [depth= 1] . ( 5 sec) [ -7967.1475] [ 1661] [depth= 1] . ( 6 sec) [ -7967.1068] [ 1665] [depth= 1] . ( 6 sec) [ -7966.1981] [ 1663] [depth= 1] . ( 6 sec) [ -7962.6415] [ 1663] [depth= 1] . ( 6 sec) [ -7962.0784] [ 1666] [depth= 1] . ( 6 sec) [ -7922.6504] [ 1615] [depth= 2] . ( 7 sec) [ -7919.3189] [ 1612] [depth= 1] . ( 7 sec) [ -7918.2260] [ 1609] [depth= 1] . ( 7 sec) [ -7916.9334] [ 1611] [depth= 1] . ( 7 sec) [ -7916.9154] [ 1613] [depth= 1] . ( 7 sec) [ -7915.8748] [ 1613] [depth= 1] . ( 7 sec) [ -7915.1461] [ 1611] [depth= 1] . ( 7 sec) [ -7914.2572] [ 1612] [depth= 1] . ( 7 sec) [ -7912.9422] [ 1614] [depth= 1] . ( 7 sec) [ -7912.4826] [ 1614] [depth= 1] . ( 7 sec) [ -7911.1546] [ 1616] [depth= 1] . ( 8 sec) [ -7897.8386] [Branch lengths ] . ( 8 sec) [ -7897.6904] [GTR parameters ] . ( 8 sec) [ -7897.0567] [Alpha ][ 0.868423] . ( 9 sec) [ -7896.8968] [ 1616] [depth= 1] . ( 10 sec) [ -7896.8701] [ 1619] [depth= 1] . ( 11 sec) [ -7896.6384] [Branch lengths ] . ( 12 sec) [ -7896.6356] [GTR parameters ] . ( 12 sec) [ -7896.6355] [Alpha ][ 0.869546] . ( 29 sec) [ -7896.6264] [Branch lengths ] . ( 29 sec) [ -7896.6264] [Topology ] . ( 30 sec) [ -7896.5945] [Topology ] . ( 30 sec) [ -7896.5733] [Topology ] . ( 31 sec) [ -7896.5699] [Topology ] . ( 32 sec) [ -7896.5690] [Topology ] . ( 32 sec) [ -7896.5689] [GTR parameters ] . ( 32 sec) [ -7896.5688] [Alpha ][ 0.870416] . ( 32 sec) [ -7896.5688] [Topology ] . ( 33 sec) [ -7896.5685] [Topology ] . ( 33 sec) [ -7896.5685] [GTR parameters ] . ( 33 sec) [ -7896.5685] [Alpha ][ 0.870416] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7896.568531. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20894.0357] [GTR parameters ] . ( 1 sec) [ -20508.1915] [Alpha ][ 0.500960] . ( 1 sec) [ -20079.9873] [ 3768] [depth= 8] . ( 1 sec) [ -19926.4215] [ 3749] [depth= 8] . ( 1 sec) [ -19906.5487] [ 3744] [depth= 2] . ( 1 sec) [ -19876.7692] [ 3742] [depth= 4] . ( 1 sec) [ -19632.4943] [ 3701] [depth= 7] . ( 1 sec) [ -19542.4823] [ 3697] [depth= 4] . ( 2 sec) [ -19319.3738] [ 3622] [depth= 17] . ( 2 sec) [ -19169.2006] [ 3597] [depth= 11] . ( 2 sec) [ -18840.9113] [ 3530] [depth= 9] . ( 2 sec) [ -18582.0615] [ 3478] [depth= 14] . ( 2 sec) [ -18261.9959] [ 3396] [depth= 8] . ( 2 sec) [ -17743.4374] [ 3328] [depth= 18] . ( 2 sec) [ -17590.5630] [ 3292] [depth= 1] . ( 2 sec) [ -17457.1331] [ 3265] [depth= 12] . ( 2 sec) [ -17357.8073] [ 3214] [depth= 2] . ( 2 sec) [ -17078.5794] [ 3207] [depth= 1] . ( 2 sec) [ -16699.1852] [ 3133] [depth= 3] . ( 2 sec) [ -16469.8125] [ 3094] [depth= 8] . ( 2 sec) [ -15796.4015] [ 2964] [depth= 7] . ( 2 sec) [ -15762.1966] [ 2955] [depth= 1] . ( 2 sec) [ -15504.7935] [ 2908] [depth= 11] . ( 2 sec) [ -15285.0340] [ 2844] [depth= 10] . ( 2 sec) [ -15081.0606] [ 2812] [depth= 7] . ( 2 sec) [ -14570.3044] [ 2720] [depth= 3] . ( 2 sec) [ -14400.1065] [ 2651] [depth= 9] . ( 2 sec) [ -12656.1550] [ 2602] [depth= 8] . ( 2 sec) [ -12647.9419] [ 2596] [depth= 1] . ( 2 sec) [ -12435.5382] [ 2537] [depth= 6] . ( 2 sec) [ -11862.6184] [ 2457] [depth= 9] . ( 3 sec) [ -11604.8103] [ 2380] [depth= 7] . ( 3 sec) [ -11291.7758] [ 2298] [depth= 8] . ( 3 sec) [ -11216.1897] [ 2272] [depth= 1] . ( 3 sec) [ -11171.1622] [ 2250] [depth= 5] . ( 3 sec) [ -10454.8716] [ 2257] [depth= 11] . ( 3 sec) [ -10386.8993] [ 2206] [depth= 2] . ( 3 sec) [ -10329.5930] [ 2193] [depth= 9] . ( 3 sec) [ -10264.6002] [ 2179] [depth= 8] . ( 3 sec) [ -10250.0620] [ 2176] [depth= 1] . ( 3 sec) [ -10221.5424] [ 2153] [depth= 1] . ( 3 sec) [ -10120.2403] [ 2125] [depth= 5] . ( 3 sec) [ -10085.4713] [ 2086] [depth= 2] . ( 3 sec) [ -10063.8893] [ 2089] [depth= 1] . ( 3 sec) [ -9944.8905] [ 2031] [depth= 3] . ( 3 sec) [ -9944.6666] [ 2033] [depth= 1] . ( 3 sec) [ -9781.6919] [ 1999] [depth= 2] . ( 3 sec) [ -9776.5040] [ 1997] [depth= 1] . ( 3 sec) [ -9659.8622] [ 1908] [depth= 3] . ( 3 sec) [ -9598.0404] [ 1896] [depth= 1] . ( 3 sec) [ -9538.5123] [ 1872] [depth= 1] . ( 3 sec) [ -9292.4814] [ 1791] [depth= 6] . ( 3 sec) [ -9264.7866] [ 1776] [depth= 1] . ( 4 sec) [ -9178.2752] [ 1754] [depth= 2] . ( 4 sec) [ -9020.7507] [ 1716] [depth= 4] . ( 4 sec) [ -8507.9932] [ 1714] [depth= 1] . ( 4 sec) [ -8494.3800] [ 1715] [depth= 6] . ( 4 sec) [ -8433.4586] [ 1715] [depth= 1] . ( 4 sec) [ -8388.8660] [ 1731] [depth= 1] . ( 4 sec) [ -8333.8643] [ 1700] [depth= 5] . ( 4 sec) [ -8314.8745] [ 1679] [depth= 1] . ( 4 sec) [ -8296.8380] [ 1678] [depth= 1] . ( 4 sec) [ -8255.5483] [ 1662] [depth= 2] . ( 4 sec) [ -8216.9417] [ 1684] [depth= 1] . ( 4 sec) [ -8162.3421] [ 1682] [depth= 1] . ( 4 sec) [ -8155.6341] [ 1686] [depth= 1] . ( 4 sec) [ -8153.0757] [ 1685] [depth= 1] . ( 4 sec) [ -8144.1308] [ 1685] [depth= 1] . ( 4 sec) [ -8119.7960] [ 1671] [depth= 2] . ( 4 sec) [ -8114.6574] [ 1673] [depth= 1] . ( 4 sec) [ -8110.3077] [ 1645] [depth= 2] . ( 5 sec) [ -8107.4755] [ 1646] [depth= 1] . ( 5 sec) [ -8007.1936] [Branch lengths ] . ( 5 sec) [ -8004.2343] [GTR parameters ] . ( 5 sec) [ -7984.2283] [Alpha ][ 0.812516] . ( 6 sec) [ -7971.9537] [ 1619] [depth= 1] . ( 6 sec) [ -7947.9716] [ 1616] [depth= 1] . ( 6 sec) [ -7946.9785] [ 1617] [depth= 1] . ( 6 sec) [ -7935.4113] [ 1613] [depth= 2] . ( 6 sec) [ -7925.3842] [ 1613] [depth= 1] . ( 6 sec) [ -7920.9127] [ 1613] [depth= 1] . ( 6 sec) [ -7920.6212] [ 1613] [depth= 1] . ( 6 sec) [ -7920.4132] [ 1614] [depth= 1] . ( 6 sec) [ -7920.3195] [ 1614] [depth= 1] . ( 7 sec) [ -7920.2998] [ 1616] [depth= 1] . ( 7 sec) [ -7915.9976] [ 1618] [depth= 1] . ( 7 sec) [ -7914.4251] [ 1615] [depth= 1] . ( 7 sec) [ -7912.6692] [ 1618] [depth= 1] . ( 8 sec) [ -7911.4005] [ 1619] [depth= 1] . ( 8 sec) [ -7909.8085] [ 1624] [depth= 1] . ( 8 sec) [ -7897.6329] [Branch lengths ] . ( 9 sec) [ -7897.6094] [GTR parameters ] . ( 9 sec) [ -7897.3430] [Alpha ][ 0.860762] . ( 11 sec) [ -7897.3182] [ 1621] [depth= 1] . ( 12 sec) [ -7896.5226] [Branch lengths ] . ( 12 sec) [ -7896.5215] [GTR parameters ] . ( 12 sec) [ -7896.5194] [Alpha ][ 0.865235] . ( 17 sec) [ -7896.4685] [ 1619] [depth= 1] . ( 29 sec) [ -7896.3736] [Branch lengths ] . ( 30 sec) [ -7896.3733] [GTR parameters ] . ( 30 sec) [ -7896.3730] [Alpha ][ 0.866859] . ( 30 sec) [ -7896.3730] [Topology ] . ( 31 sec) [ -7896.3691] [Topology ] . ( 31 sec) [ -7896.3681] [Topology ] . ( 32 sec) [ -7896.3677] [Topology ] . ( 32 sec) [ -7896.3676] [GTR parameters ] . ( 32 sec) [ -7896.3676] [Alpha ][ 0.867726] . ( 32 sec) [ -7896.3676] [Topology ] . ( 33 sec) [ -7896.3674] [Topology ] . ( 33 sec) [ -7896.3674] [GTR parameters ] . ( 33 sec) [ -7896.3674] [Alpha ][ 0.867726] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7896.367409. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20578.6199] [GTR parameters ] . ( 1 sec) [ -20245.5711] [Alpha ][ 0.500960] . ( 1 sec) [ -19759.9835] [ 3639] [depth= 8] . ( 1 sec) [ -19381.3910] [ 3573] [depth= 5] . ( 1 sec) [ -16420.3188] [ 3518] [depth= 9] . ( 1 sec) [ -16250.1581] [ 3491] [depth= 1] . ( 1 sec) [ -15508.7001] [ 3444] [depth= 3] . ( 1 sec) [ -15496.9653] [ 3438] [depth= 1] . ( 1 sec) [ -15322.1839] [ 3434] [depth= 5] . ( 1 sec) [ -15168.3228] [ 3394] [depth= 3] . ( 1 sec) [ -15009.9359] [ 3388] [depth= 2] . ( 1 sec) [ -14786.8915] [ 3378] [depth= 4] . ( 1 sec) [ -14565.1274] [ 3308] [depth= 1] . ( 1 sec) [ -14314.8241] [ 3301] [depth= 14] . ( 1 sec) [ -14179.4470] [ 3298] [depth= 1] . ( 1 sec) [ -14070.1565] [ 3260] [depth= 15] . ( 1 sec) [ -14042.7953] [ 3259] [depth= 1] . ( 1 sec) [ -13839.5557] [ 3245] [depth= 2] . ( 1 sec) [ -13623.5940] [ 3184] [depth= 1] . ( 1 sec) [ -13427.7703] [ 3120] [depth= 19] . ( 1 sec) [ -13197.8444] [ 3089] [depth= 11] . ( 1 sec) [ -13134.7000] [ 3086] [depth= 3] . ( 2 sec) [ -13000.4347] [ 3048] [depth= 6] . ( 2 sec) [ -12978.3348] [ 3030] [depth= 1] . ( 2 sec) [ -12914.5022] [ 3024] [depth= 3] . ( 2 sec) [ -12646.0365] [ 2986] [depth= 7] . ( 2 sec) [ -12527.8798] [ 2947] [depth= 3] . ( 2 sec) [ -12123.5002] [ 2822] [depth= 11] . ( 2 sec) [ -11917.7018] [ 2772] [depth= 15] . ( 2 sec) [ -11878.2162] [ 2753] [depth= 1] . ( 2 sec) [ -11755.6649] [ 2720] [depth= 1] . ( 2 sec) [ -11722.7479] [ 2708] [depth= 2] . ( 2 sec) [ -11489.8096] [ 2594] [depth= 10] . ( 2 sec) [ -11360.1178] [ 2586] [depth= 1] . ( 2 sec) [ -11261.1411] [ 2549] [depth= 1] . ( 2 sec) [ -11245.8667] [ 2543] [depth= 1] . ( 2 sec) [ -11161.8565] [ 2506] [depth= 15] . ( 2 sec) [ -11121.6404] [ 2485] [depth= 2] . ( 2 sec) [ -10953.9073] [ 2438] [depth= 6] . ( 2 sec) [ -10953.1288] [ 2441] [depth= 3] . ( 2 sec) [ -10887.6698] [ 2429] [depth= 13] . ( 2 sec) [ -10865.6518] [ 2411] [depth= 4] . ( 3 sec) [ -10861.8624] [ 2409] [depth= 3] . ( 3 sec) [ -10815.1893] [ 2406] [depth= 1] . ( 3 sec) [ -10695.3929] [ 2352] [depth= 6] . ( 3 sec) [ -10630.8158] [ 2349] [depth= 3] . ( 3 sec) [ -10447.9983] [ 2296] [depth= 3] . ( 3 sec) [ -10194.9153] [ 2207] [depth= 4] . ( 3 sec) [ -9993.6005] [ 2141] [depth= 8] . ( 3 sec) [ -9888.2632] [ 2145] [depth= 1] . ( 3 sec) [ -9710.9159] [ 2123] [depth= 1] . ( 3 sec) [ -9650.0753] [ 2095] [depth= 2] . ( 3 sec) [ -9615.2100] [ 2091] [depth= 1] . ( 3 sec) [ -9591.3174] [ 2064] [depth= 1] . ( 3 sec) [ -9588.7379] [ 2064] [depth= 1] . ( 3 sec) [ -9573.9815] [ 2064] [depth= 1] . ( 3 sec) [ -9537.8881] [ 2071] [depth= 1] . ( 3 sec) [ -9374.8716] [ 2038] [depth= 2] . ( 3 sec) [ -9371.4247] [ 2041] [depth= 2] . ( 3 sec) [ -9369.0251] [ 2041] [depth= 1] . ( 3 sec) [ -9368.9501] [ 2027] [depth= 2] . ( 3 sec) [ -9002.8395] [ 1973] [depth= 5] . ( 4 sec) [ -8947.1085] [ 1929] [depth= 3] . ( 4 sec) [ -8826.9572] [ 1930] [depth= 1] . ( 4 sec) [ -8787.9605] [ 1896] [depth= 6] . ( 4 sec) [ -8692.0876] [ 1938] [depth= 2] . ( 4 sec) [ -8689.9178] [ 1935] [depth= 1] . ( 4 sec) [ -8615.3402] [ 1848] [depth= 4] . ( 4 sec) [ -8543.0429] [ 1860] [depth= 4] . ( 4 sec) [ -8539.8028] [ 1855] [depth= 1] . ( 4 sec) [ -8531.9750] [ 1854] [depth= 1] . ( 4 sec) [ -8485.6113] [ 1846] [depth= 4] . ( 4 sec) [ -8444.0577] [ 1844] [depth= 1] . ( 4 sec) [ -8435.2019] [ 1846] [depth= 1] . ( 4 sec) [ -8416.4982] [ 1836] [depth= 2] . ( 4 sec) [ -8412.7442] [ 1836] [depth= 1] . ( 4 sec) [ -8406.4335] [ 1838] [depth= 2] . ( 4 sec) [ -8400.0234] [ 1839] [depth= 1] . ( 4 sec) [ -8285.6512] [Branch lengths ] . ( 5 sec) [ -8283.4237] [GTR parameters ] . ( 5 sec) [ -8270.0129] [Alpha ][ 0.728170] . ( 5 sec) [ -8261.9630] [ 1826] [depth= 1] . ( 5 sec) [ -8238.7892] [ 1809] [depth= 3] . ( 6 sec) [ -8238.4570] [ 1812] [depth= 2] . ( 6 sec) [ -8214.6423] [ 1791] [depth= 1] . ( 6 sec) [ -8213.8099] [ 1786] [depth= 2] . ( 6 sec) [ -8174.5696] [ 1756] [depth= 4] . ( 6 sec) [ -8155.9841] [ 1731] [depth= 1] . ( 6 sec) [ -8155.1082] [ 1730] [depth= 1] . ( 6 sec) [ -8013.9563] [ 1666] [depth= 5] . ( 6 sec) [ -8013.8123] [ 1665] [depth= 1] . ( 6 sec) [ -8012.2368] [ 1669] [depth= 1] . ( 7 sec) [ -8011.3312] [ 1670] [depth= 1] . ( 7 sec) [ -8007.4579] [ 1658] [depth= 2] . ( 7 sec) [ -7964.8629] [ 1641] [depth= 2] . ( 7 sec) [ -7964.6371] [ 1641] [depth= 1] . ( 7 sec) [ -7964.6006] [ 1641] [depth= 1] . ( 7 sec) [ -7938.1470] [ 1627] [depth= 3] . ( 8 sec) [ -7923.5121] [ 1614] [depth= 1] . ( 8 sec) [ -7922.1459] [ 1617] [depth= 1] . ( 8 sec) [ -7922.0703] [ 1618] [depth= 2] . ( 8 sec) [ -7921.6704] [ 1620] [depth= 1] . ( 8 sec) [ -7901.0039] [Branch lengths ] . ( 9 sec) [ -7900.3881] [GTR parameters ] . ( 9 sec) [ -7898.2805] [Alpha ][ 0.856129] . ( 9 sec) [ -7898.2544] [ 1618] [depth= 1] . ( 9 sec) [ -7898.1302] [ 1619] [depth= 2] . ( 11 sec) [ -7898.0776] [ 1617] [depth= 1] . ( 11 sec) [ -7898.0548] [ 1614] [depth= 1] . ( 12 sec) [ -7896.8600] [Branch lengths ] . ( 12 sec) [ -7896.8588] [GTR parameters ] . ( 12 sec) [ -7896.8455] [Alpha ][ 0.867540] . ( 12 sec) [ -7896.7530] [ 1619] [depth= 1] . ( 15 sec) [ -7896.6420] [Branch lengths ] . ( 15 sec) [ -7896.6419] [GTR parameters ] . ( 15 sec) [ -7896.6418] [Alpha ][ 0.868449] . ( 32 sec) [ -7896.6280] [Branch lengths ] . ( 32 sec) [ -7896.6280] [Topology ] . ( 33 sec) [ -7896.5947] [Topology ] . ( 34 sec) [ -7896.5735] [Topology ] . ( 34 sec) [ -7896.5702] [Topology ] . ( 35 sec) [ -7896.5694] [Topology ] . ( 35 sec) [ -7896.5691] [GTR parameters ] . ( 35 sec) [ -7896.5688] [Alpha ][ 0.870258] . ( 35 sec) [ -7896.5688] [Topology ] . ( 36 sec) [ -7896.5685] [Topology ] . ( 36 sec) [ -7896.5685] [GTR parameters ] . ( 36 sec) [ -7896.5685] [Alpha ][ 0.870258] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7896.568510. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18045.8250] [GTR parameters ] . ( 0 sec) [ -17669.9658] [Alpha ][ 0.500960] . ( 0 sec) [ -17243.4157] [ 3718] [depth= 6] . ( 0 sec) [ -16910.7638] [ 3684] [depth= 8] . ( 0 sec) [ -16625.6134] [ 3660] [depth= 6] . ( 0 sec) [ -16505.1075] [ 3658] [depth= 6] . ( 0 sec) [ -16361.5292] [ 3651] [depth= 1] . ( 1 sec) [ -16336.1525] [ 3652] [depth= 5] . ( 1 sec) [ -16269.9927] [ 3632] [depth= 6] . ( 1 sec) [ -16098.2782] [ 3577] [depth= 4] . ( 1 sec) [ -15984.0639] [ 3547] [depth= 8] . ( 1 sec) [ -15794.9673] [ 3510] [depth= 1] . ( 1 sec) [ -15576.2512] [ 3469] [depth= 17] . ( 1 sec) [ -15445.0199] [ 3458] [depth= 2] . ( 1 sec) [ -15435.6443] [ 3448] [depth= 1] . ( 1 sec) [ -15270.1665] [ 3414] [depth= 7] . ( 1 sec) [ -15077.9977] [ 3417] [depth= 13] . ( 1 sec) [ -15008.8036] [ 3415] [depth= 2] . ( 1 sec) [ -14878.2264] [ 3383] [depth= 8] . ( 1 sec) [ -14830.5612] [ 3380] [depth= 3] . ( 1 sec) [ -14606.0791] [ 3327] [depth= 8] . ( 1 sec) [ -14325.5160] [ 3244] [depth= 12] . ( 1 sec) [ -14092.2766] [ 3151] [depth= 6] . ( 1 sec) [ -14057.5378] [ 3108] [depth= 1] . ( 1 sec) [ -14034.4945] [ 3100] [depth= 1] . ( 1 sec) [ -13720.8095] [ 3016] [depth= 8] . ( 1 sec) [ -13716.8317] [ 3017] [depth= 1] . ( 1 sec) [ -13644.7674] [ 2995] [depth= 1] . ( 1 sec) [ -13643.6685] [ 2994] [depth= 1] . ( 1 sec) [ -13132.9810] [ 2918] [depth= 9] . ( 2 sec) [ -13025.8366] [ 2910] [depth= 1] . ( 2 sec) [ -12826.4193] [ 2872] [depth= 3] . ( 2 sec) [ -12522.4651] [ 2800] [depth= 2] . ( 2 sec) [ -12405.4422] [ 2759] [depth= 1] . ( 2 sec) [ -12130.3301] [ 2666] [depth= 8] . ( 2 sec) [ -11842.1362] [ 2617] [depth= 3] . ( 2 sec) [ -11706.9173] [ 2595] [depth= 4] . ( 2 sec) [ -11411.3195] [ 2492] [depth= 8] . ( 2 sec) [ -11384.6611] [ 2496] [depth= 1] . ( 2 sec) [ -11309.8424] [ 2471] [depth= 1] . ( 2 sec) [ -11263.4718] [ 2437] [depth= 1] . ( 2 sec) [ -11188.8134] [ 2399] [depth= 5] . ( 2 sec) [ -11107.9553] [ 2446] [depth= 1] . ( 2 sec) [ -10933.4336] [ 2388] [depth= 7] . ( 2 sec) [ -10771.7234] [ 2303] [depth= 2] . ( 2 sec) [ -10508.2561] [ 2282] [depth= 5] . ( 2 sec) [ -10456.6197] [ 2211] [depth= 7] . ( 2 sec) [ -10452.8019] [ 2216] [depth= 1] . ( 2 sec) [ -10291.2004] [ 2193] [depth= 5] . ( 2 sec) [ -10276.7545] [ 2197] [depth= 4] . ( 2 sec) [ -10255.4891] [ 2192] [depth= 2] . ( 3 sec) [ -9777.7780] [ 2173] [depth= 5] . ( 3 sec) [ -9715.6706] [ 2168] [depth= 1] . ( 3 sec) [ -9622.9388] [ 2152] [depth= 1] . ( 3 sec) [ -9600.8278] [ 2146] [depth= 1] . ( 3 sec) [ -9518.4309] [ 2146] [depth= 1] . ( 3 sec) [ -9500.1061] [ 2111] [depth= 1] . ( 3 sec) [ -9492.8450] [ 2116] [depth= 4] . ( 3 sec) [ -9406.1217] [ 2036] [depth= 3] . ( 3 sec) [ -9138.6772] [ 1958] [depth= 4] . ( 3 sec) [ -9138.1671] [ 1962] [depth= 1] . ( 3 sec) [ -9134.2993] [ 1962] [depth= 2] . ( 3 sec) [ -9093.4535] [ 1966] [depth= 1] . ( 3 sec) [ -9074.0859] [ 1956] [depth= 1] . ( 3 sec) [ -9035.5670] [ 1954] [depth= 1] . ( 3 sec) [ -8996.1265] [ 1954] [depth= 1] . ( 3 sec) [ -8798.6854] [ 1942] [depth= 3] . ( 3 sec) [ -8676.2749] [ 1870] [depth= 3] . ( 3 sec) [ -8675.6327] [ 1870] [depth= 1] . ( 3 sec) [ -8635.8722] [ 1868] [depth= 4] . ( 3 sec) [ -8630.2000] [ 1869] [depth= 1] . ( 3 sec) [ -8612.8395] [ 1867] [depth= 2] . ( 3 sec) [ -8606.7732] [ 1863] [depth= 1] . ( 3 sec) [ -8587.8222] [ 1857] [depth= 2] . ( 4 sec) [ -8579.4530] [ 1856] [depth= 1] . ( 4 sec) [ -8490.5739] [ 1839] [depth= 3] . ( 4 sec) [ -8486.4075] [ 1843] [depth= 1] . ( 4 sec) [ -8482.1341] [ 1817] [depth= 4] . ( 4 sec) [ -8455.3453] [ 1796] [depth= 2] . ( 4 sec) [ -8455.0754] [ 1796] [depth= 1] . ( 4 sec) [ -8353.1016] [ 1758] [depth= 2] . ( 4 sec) [ -8351.2194] [ 1757] [depth= 1] . ( 4 sec) [ -8332.6702] [ 1756] [depth= 3] . ( 4 sec) [ -8321.3261] [ 1755] [depth= 1] . ( 4 sec) [ -8167.8854] [Branch lengths ] . ( 5 sec) [ -8165.0912] [GTR parameters ] . ( 5 sec) [ -8147.4112] [Alpha ][ 0.776830] . ( 5 sec) [ -8137.9347] [ 1757] [depth= 2] . ( 5 sec) [ -8092.3191] [ 1731] [depth= 1] . ( 5 sec) [ -8092.0250] [ 1732] [depth= 1] . ( 5 sec) [ -8090.8146] [ 1729] [depth= 1] . ( 5 sec) [ -8083.0905] [ 1714] [depth= 1] . ( 5 sec) [ -8071.5309] [ 1712] [depth= 2] . ( 5 sec) [ -8047.2166] [ 1699] [depth= 1] . ( 5 sec) [ -8014.7897] [ 1678] [depth= 1] . ( 6 sec) [ -8013.2960] [ 1677] [depth= 1] . ( 6 sec) [ -8013.0094] [ 1677] [depth= 2] . ( 6 sec) [ -7975.4472] [ 1663] [depth= 1] . ( 6 sec) [ -7921.5804] [ 1613] [depth= 7] . ( 6 sec) [ -7921.4284] [ 1613] [depth= 1] . ( 6 sec) [ -7919.9732] [ 1616] [depth= 1] . ( 6 sec) [ -7917.9829] [ 1614] [depth= 1] . ( 6 sec) [ -7915.6369] [ 1615] [depth= 1] . ( 7 sec) [ -7915.5853] [ 1615] [depth= 1] . ( 7 sec) [ -7915.0825] [ 1618] [depth= 2] . ( 7 sec) [ -7914.3014] [ 1614] [depth= 1] . ( 7 sec) [ -7913.4184] [ 1616] [depth= 1] . ( 7 sec) [ -7912.8344] [ 1620] [depth= 1] . ( 7 sec) [ -7912.2672] [ 1625] [depth= 2] . ( 8 sec) [ -7911.0208] [ 1621] [depth= 1] . ( 8 sec) [ -7898.5628] [Branch lengths ] . ( 8 sec) [ -7898.4146] [GTR parameters ] . ( 8 sec) [ -7897.6998] [Alpha ][ 0.853437] . ( 9 sec) [ -7897.6872] [ 1621] [depth= 1] . ( 11 sec) [ -7897.5985] [ 1617] [depth= 1] . ( 11 sec) [ -7896.8367] [Branch lengths ] . ( 11 sec) [ -7896.8351] [GTR parameters ] . ( 11 sec) [ -7896.8188] [Alpha ][ 0.866002] . ( 21 sec) [ -7896.5336] [ 1619] [depth= 2] . ( 29 sec) [ -7896.3768] [Branch lengths ] . ( 29 sec) [ -7896.3741] [GTR parameters ] . ( 29 sec) [ -7896.3741] [Alpha ][ 0.866868] . ( 29 sec) [ -7896.3741] [Topology ] . ( 30 sec) [ -7896.3690] [Topology ] . ( 31 sec) [ -7896.3679] [Topology ] . ( 31 sec) [ -7896.3675] [Topology ] . ( 32 sec) [ -7896.3675] [GTR parameters ] . ( 32 sec) [ -7896.3675] [Alpha ][ 0.867735] . ( 32 sec) [ -7896.3675] [Topology ] . ( 32 sec) [ -7896.3673] [Topology ] . ( 33 sec) [ -7896.3673] [GTR parameters ] . ( 33 sec) [ -7896.3673] [Alpha ][ 0.867735] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7896.367288. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7943.507673 . ( 1 sec) [ -7939.9700] [GTR parameters ] . ( 1 sec) [ -7937.9644] [Alpha ][ 0.846040] . ( 1 sec) [ -7937.9644] [Topology ] . ( 2 sec) [ -7904.9970] [Topology ] . ( 2 sec) [ -7899.3218] [Topology ] . ( 3 sec) [ -7897.8608] [Topology ] . ( 4 sec) [ -7897.2441] [Topology ] . ( 5 sec) [ -7896.9520] [Topology ] . ( 5 sec) [ -7896.8081] [Topology ] . ( 6 sec) [ -7896.7358] [Topology ] . ( 7 sec) [ -7896.6992] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7896.699227 . ( 12 sec) [ -7896.6594] [GTR parameters ] . ( 13 sec) [ -7896.5871] [Alpha ][ 0.871821] . ( 13 sec) [ -7896.5871] [Topology ] . ( 13 sec) [ -7896.5615] [Topology ] . ( 14 sec) [ -7896.5494] [Topology ] . ( 15 sec) [ -7896.5433] [Topology ] . ( 16 sec) [ -7896.5403] [Topology ] . ( 16 sec) [ -7896.5387] [Topology ] . ( 17 sec) [ -7896.5379] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7896.537893 . ( 23 sec) [ -7896.5379] [GTR parameters ] . ( 23 sec) [ -7896.5374] [Alpha ][ 0.873929] . ( 23 sec) [ -7896.5374] [Topology ] . ( 23 sec) [ -7896.5369] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 35 sec) [ -7939.9700] [GTR parameters ] . ( 35 sec) [ -7937.9644] [Alpha ][ 0.846040] . ( 35 sec) [ -7934.8492] [ 1615] [depth= 1] . ( 35 sec) [ -7930.6520] [ 1640] [depth= 2] . ( 36 sec) [ -7929.7377] [ 1641] [depth= 1] . ( 36 sec) [ -7927.4369] [ 1640] [depth= 1] . ( 37 sec) [ -7927.0405] [ 1641] [depth= 1] . ( 37 sec) [ -7924.5552] [ 1640] [depth= 1] . ( 37 sec) [ -7922.1555] [ 1638] [depth= 1] . ( 37 sec) [ -7921.0597] [ 1638] [depth= 1] . ( 37 sec) [ -7920.5539] [ 1641] [depth= 2] . ( 37 sec) [ -7918.6026] [ 1643] [depth= 1] . ( 37 sec) [ -7918.4087] [ 1645] [depth= 1] . ( 37 sec) [ -7916.1650] [ 1643] [depth= 1] . ( 37 sec) [ -7914.2709] [ 1646] [depth= 1] . ( 38 sec) [ -7902.3233] [Branch lengths ] . ( 38 sec) [ -7902.2813] [GTR parameters ] . ( 38 sec) [ -7902.2779] [Alpha ][ 0.851645] . ( 39 sec) [ -7902.1786] [ 1643] [depth= 1] . ( 39 sec) [ -7900.1373] [ 1618] [depth= 2] . ( 39 sec) [ -7900.1078] [ 1619] [depth= 1] . ( 41 sec) [ -7900.0651] [ 1621] [depth= 1] . ( 41 sec) [ -7896.9257] [Branch lengths ] . ( 42 sec) [ -7896.9155] [GTR parameters ] . ( 42 sec) [ -7896.8794] [Alpha ][ 0.870496] . ( 44 sec) [ -7896.6762] [ 1624] [depth= 1] . ( 45 sec) [ -7896.5537] [Branch lengths ] . ( 45 sec) [ -7896.5534] [GTR parameters ] . ( 45 sec) [ -7896.5522] [Alpha ][ 0.866934] . ( 56 sec) [ -7896.5090] [ 1622] [depth= 1] . ( 62 sec) [ -7896.4323] [Branch lengths ] . ( 62 sec) [ -7896.4322] [GTR parameters ] . ( 62 sec) [ -7896.4322] [Alpha ][ 0.866068] . ( 62 sec) [ -7896.4322] [Topology ] . ( 63 sec) [ -7896.3948] [Topology ] . ( 63 sec) [ -7896.3725] [Topology ] . ( 64 sec) [ -7896.3689] [Topology ] . ( 65 sec) [ -7896.3679] [Topology ] . ( 66 sec) [ -7896.3676] [Topology ] . ( 66 sec) [ -7896.3675] [GTR parameters ] . ( 66 sec) [ -7896.3672] [Alpha ][ 0.867513] . ( 66 sec) [ -7896.3672] [Topology ] . ( 67 sec) [ -7896.3671] [Topology ] . ( 67 sec) [ -7896.3671] [GTR parameters ] . ( 67 sec) [ -7896.3671] [Alpha ][ 0.867513] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7896.536936 . Log likelihood obtained after SPR moves : -7896.367109 . Log likelihood of the current tree: -7896.367109. . Printing the most likely tree in file 'data87.phy_phyml_tree.txt'... . Best log likelihood : -7896.367109 . Time used 0h1m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo